PROJECT SUMMARY Rhinovirus causes the common cold and is especially dangerous for asthmatics, whose airway epithelial cells display a compromised response to the virus. Our long-term goal is to characterize the antiviral response of lung epithelia and use this knowledge to normalize its function in asthma. Long non-coding RNAs (lncRNAs) can be potent transcriptional regulators of the antiviral response, however their role in regulating the response of airway epithelia cells to rhinovirus is completely unknown. We hypothesize that bronchial epithelial cell lncRNAs control the antiviral response to rhinovirus and that lncRNA dysregulation contributes to asthma pathogenesis. Using 3D organotypic air-liquid interface (ALI) cultures of primary human bronchial epithelia cells (BECs) from healthy and asthmatic donors infected with rhinovirus, we have identified lung antiviral response lncRNAs and lncRNAs that are differentially expressed between healthy and asthmatic donors. This unique catalog of curated lncRNAs provides a candidate pool from which important regulatory lncRNAs could be identified, characterized and potentially exploited for asthma diagnosis and treatment. In Aim 1 we will identify where candidate lncRNA transcripts reside in the cell and will determine what innate sensors control their expression. These experiments will inform mechanistic studies by identifying the cellular compartment in which these transcripts function, and pathways that regulate their expression. In Aim 2 we will use CRISPR/Cas9 epigenome?editing technology to silence expression of lncRNAs in cell lines and primary human BECs grown in ALI culture. Using this approach we can test lncRNA function during rhinovirus infection under conditions that closely recapitulate the complexity of the airway epithelium in vivo. By measuring multiple aspects of the airway epithelium that are impacted by rhinovirus infection, we will be able to define the function of each lncRNA in the antiviral response. Impact: These studies will identify gene-regulatory mechanisms controlling innate immune responses in the lung epithelium, which could have far reaching implications in our understanding of asthma pathogenesis and in the design of disease intervention strategies. On completion, we will have a detailed molecular understanding of where in the cell these lncRNAs are expressed during rhinovirus infection and what molecular signals control their expression. We will also have determined whether these lncRNAs contribute to the antiviral response to rhinovirus in primary human airway epithelial cells. These results will provide a necessary foundation for additional investigations into the molecular mechanisms used by lncRNAs to regulate antiviral responses. Since lncRNAs have exquisite cell-type specificity, this work may also identify exciting novel targets for new intervention strategies.